Diagnosis and treatment of invasive aspergillosis

ABSTRACT

Methods for diagnosing, treating, and monitoring the treatment of invasive aspergillosis (IA) are described. The methods can include detecting the presence of one or more volatile organic compounds (VOCs) in the breath of subjects suspected of having IA.

CLAIM OF PRIORITY

This application claims the benefit of U.S. Provisional PatentApplication Ser. Nos. 62/008,419, filed on Jun. 5, 2014, and 62/050,583,filed on Sep. 15, 2014. The entire contents of the foregoing are herebyincorporated by reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grants No.R21AI085454 and K23AI097225 awarded by the National Institutes ofHealth. The Government has certain rights in the invention.

TECHNICAL FIELD

Provided herein are methods for diagnosing, treating, and monitoring thetreatment of invasive aspergillosis (IA). The methods can includedetecting the presence of one or more volatile organic compounds (VOCs)in the breath of subjects suspected of having IA.

BACKGROUND

IA is a common, rapidly progressive, highly morbid, and frequently fatalinfection in immunocompromised patients, especially in patients withchemotherapy-induced neutropenia or who are immunosuppressed as a resultof receiving glucocorticoid treatment for graft-versus-host disease(GVHD). Timely diagnosis with prompt initiation of appropriateantifungal therapy improves clinical outcomes. Unfortunately, clinicaland radiographic manifestations are nonspecific, and standard cultureand antigen diagnostic approaches lack sensitivity and specificity forIA. Definitive diagnosis still relies on biopsy, which is oftenunacceptably morbid and frequently uninformative in these debilitatedpatients.

SUMMARY

As described herein, the present inventors have (1) identified a unique,species-specific profile of volatile organic compounds (VOCs) producedby Aspergillus fumigatus, A. terreus, A. calidoustus, and otherpathogenic fungi in vitro that can be used to distinguish pathogenicfungal species from each other, (2) demonstrated that differentialmobility spectrometry (DMS) can be used for the rapid discriminationbetween fungal species using pattern-based detection of thesespecies-specific VOC profiles, and (3) accurately identified patientswith invasive aspergillosis (IA) via direct detection of a pattern of A.fumigatus VOCs in their breath, including a combination ofbeta-trans-bergamotene, beta-vatirenene, and trans-geranylacetone.

Thus in a first aspect, the invention provides methods for diagnosing asubject with invasive aspergillosis (IA). The methods include obtaininga sample comprising breath of a subject or headspace from a culturesuspected of comprising Aspergillus isolated from a subject; detectingthe presence in the sample of one, two, three, or more volatile organiccompounds (VOCs) produced by the Aspergillus species in a samplecomprising breath from the subject or headspace from a culture suspectedof comprising Aspergillus isolated from the subject, wherein the VOCsare selected from the group consisting of camphene, α-pinene, β-pinene,limonene, α-trans-bergamotene, β-trans-bergamotene,trans-geranylacetone, beta-trans-bergamotene, beta-vatirenene,trans-geranylacetone, camphene, alpha-pinene, beta-pinene, limonene,alpha-bergamotene, beta-trans-bergamotene, elixene, alpha-santalene,beta-elemene, acoradien, chamigrene, 1,5,9-trimethyl cyclododecatriene,9-decene-2-one and beta-sesquiphellandrene; and diagnosing a subject ashaving IA based on the presence of (i.e., when there are) one, two,three or more of the VOCs in the sample.

In some embodiments, the methods include detecting the presence in thesample of one, two or three VOCs selected from the group consisting ofcamphene, α-pinene, β-pinene, limonene, α-trans-bergamotene,β-trans-bergamotene, trans-geranylacetone, beta-trans-bergamotene,beta-vatirenene and trans-geranylacetone; and diagnosing a subject whohas one, two or all three of beta-trans-bergamotene, beta-vatirenene andtrans-geranylacetone in the sample as having IA. In preferredembodiments, a diagnosis of IA is based on the presence of all three ofthe VOCs α-trans-bergamotene, β-trans-bergamotene, andtrans-geranylacetone in the sample.

In another aspect, the invention provides methods for treating a subjectwho has invasive aspergillosis (IA). The methods include obtaining asample comprising breath of a subject or headspace from a culturesuspected of comprising Aspergillus isolated from a subject; detectingthe presence in the sample of one, two or three VOCs selected from thegroup consisting of α-trans-bergamotene, β-trans-bergamotene,trans-geranylacetone, and administering an antifungal treatment to asubject who has one, two or all three of beta-trans-bergamotene,beta-vatirenene and trans-geranylacetone in their breath or camphene,α-pinene, β-pinene, limonene, α-trans-bergamotene, andβ-trans-bergamotene in headspace from a culture.

In some embodiments, the treatment includes administration of one ormore doses of one or more antifungal compounds, e.g., an amphotericin Bformulation; an azole compound; and an echinocandin.

In another aspect, the invention provides methods for detecting thepresence of an Aspergillus fumigatus, A. terreus, or A. calidoustusinfection in a subject. The methods include obtaining a samplecomprising breath of a subject, or headspace from a culture suspected ofcomprising Aspergillus isolated from a subject; determining the presenceof one, two, three, or more, e.g., all, of the VOCs selected from thegroup consisting of camphene, alpha-pinene, beta-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, trans-geranylacetone, elixene,alpha-santalene, beta-elemene, acoradien, chamigrene, 1,5,9-trimethylcyclododecatriene, 9-decene-2-one and beta-sesquiphellandrene in thesample. The presence of one, two, three, or more, e.g., all, ofcamphene, α-pinene, β-pinene, limonene, α-trans-bergamotene,β-trans-bergamotene in headspace, or α-trans-bergamotene,β-trans-bergamotene, and trans-geranylacetone in breath, indicates thepresence of an A. fumigatus infection; the presence of one, two, three,or more, e.g., all, of elixene, alpha-santalene, beta-elemene,acoradien, chamigrene, and 1,5,9-trimethyl cyclododecatriene indicatesthe presence of an A. terreus infection; and the presence of one or bothof 9-decene-2-one and beta-sesquiphellandrene indicates the presence ofan A. calidoustus infection in the subject.

In some embodiments, the methods include selecting, and optionallyadministering, a therapy comprising an azole, e.g., voriconazole, for asubject who has an A. fumigatus or A. terreus infection; or selecting,and optionally administering, a therapy comprising amphotericin B (AMB),e.g., D-AMB or a lipid formulation of AMB, for a subject who has an A.calidoustus infection.

In another aspect, the invention provides methods for monitoringefficacy of a treatment for invasive aspergillosis (IA) in a subject.The methods include determining a first level of one, two, three, ormore volatile organic compounds (VOCs) produced by the Aspergillusspecies in a sample comprising breath from the subject or headspace froma culture suspected of comprising Aspergillus isolated from the subject,wherein the VOCs are selected from the group consisting of camphene,alpha-pinene, beta-pinene, limonene, α-trans-bergamotene,β-trans-bergamotene, trans-geranylacetone, elixene, alpha-santalene,beta-elemene, acoradien, chamigrene, 1,5,9-trimethyl cyclododecatriene,9-decene-2-one and beta-sesquiphellandrene, in the subject;administering a treatment for IA to the subject; determining a secondlevel of the VOCs in a sample obtained after administration of thetreatment to the subject; and comparing the first and second levels ofVOCs. A decrease in the VOCs indicates that the treatment has beeneffective in treating the IA in the subject, and an increase or nochange indicates that the treatment has not been effective in treatingthe IA in the subject.

In some embodiments, the treatment includes administration of one ormore doses of one or more antifungal compounds, e.g., an amphotericin Bformulation; an azole compound; and an echinocandin.

In yet another aspect, the invention provides methods for identifying acandidate compound for the treatment of IA. The methods includeproviding a test culture comprising one or more Aspergillus species;detecting a baseline level of fungal VOCs in the headspace of theculture in the absence of the test compound, wherein the VOCs areselected from the group consisting of camphene, alpha-pinene,beta-pinene, limonene, α-trans-bergamotene, β-trans-bergamotene,trans-geranylacetone, elixene, alpha-santalene, beta-elemene, acoradien,chamigrene, 1,5,9-trimethyl cyclododecatriene, 9-decene-2-one andbeta-sesquiphellandrene, in the subject; contacting the test culturewith a test compound; determining a second level of the VOCs in a thetest culture; comparing the second level of VOCs to the baseline level;and identifying a test compound that decreases levels of fungal VOCs inthe test culture as a candidate compound for the treatment of IA.

In another aspect, the invention provides methods for detecting thepresence of an Aspergillus fumigatus, A. terreus, or A. calidoustusinfection in a culture. The methods include obtaining a sample from theculture, e.g., gas from the headspace of the culture; determining thepresence of one, two, three, or more, e.g., all, of the VOCs selectedfrom the group consisting of camphene, alpha-pinene, beta-pinene,limonene, α-trans-bergamotene, β-trans-bergamotene,trans-geranylacetone, elixene, alpha-santalene, beta-elemene, acoradien,chamigrene, 1,5,9-trimethyl cyclododecatriene, 9-decene-2-one andbeta-sesquiphellandrene in the sample. The presence of one, two, three,or more, e.g., all, of camphene, alpha-pinene, beta-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, and/or trans-geranylacetone,indicates the presence of A. fumigatus in the culture; the presence ofone, two, three, or more, e.g., all, of elixene, alpha-santalene,beta-elemene, acoradien, chamigrene, and 1,5,9-trimethylcyclododecatriene indicates the presence of A. terreus in the culture;and the presence of one or both of 9-decene-2-one andbeta-sesquiphellandrene indicates the presence of A. calidoustusinfection in the culture.

In some embodiments of the various methods described herein, determiningthe presence of a VOC comprises assaying the sample to detect thepresence the VOC. In some embodiments, assaying the sample to detect thepresence the VOC comprises using a gas chromatography (GC) orspectrometry method. In some embodiments, the spectrophotometry methodis mobility spectrometry (IMS) or differential mobility spectrometry(DMS).

In some embodiments of the various methods described herein, the subjectis a human.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety, including especially U.S. ApplicationSer. No. 61/698,155, filed on Sep. 7, 2012, and PCT/US2013/058560, filedon Sep. 6, 2013, and published as WO 2014/039856. In case of conflict,the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from thefollowing detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1. Collection of VOCs from headspace gas of in vitro cultures orpatient breath, with concentration of VOCs on a thermal desorption trap,thermal desorption onto the GC, and parallel data acquisition on a dualmass spectrometry/differential mobility spectrometry system.

FIGS. 2A-B. A) Total ion chromatograms (TIC) generated by GC-MS ofreference and clinical strains of A. fumigatus at 96 hrs in YPD media,showing the reproducibility of the VOC profile within species. B) GC-MSTIC of common pathogenic fungal species, showing interspecies VOCprofile heterogeneity.

FIG. 3. Key features of the A. fumigatus VOC profile: A. camphene, B.α-pinene, C. β-pinene, D. limonene, E. α-bergamotene, and F.beta-trans-bergamotene.

FIG. 4. Key features of the A. terreus VOC profile: A. elixene, B.α-santalene, C. β-elemene, D. acoradien, E. chamigrene, and F.1,5,9-trimethyl cyclododecatriene.

FIG. 5. Key features of the A. calidoustus VOC profile: A.9-decene-2-one, B. β-sesquiphellandrene.

FIG. 6. Kinetics of A. fumigatus VOC emission with hyphal growth.

FIG. 7. Kinetics of A. terreus VOC emission with hyphal growth.

FIG. 8. Kinetics of A. calidoustus VOC emission with hyphal growth.

FIGS. 9A-B. Modulation of key A. fumigatus VOCs with antifungal therapy.A) GC-MS TIC of A. fumigatus with the addition of micafungin, showinginitial increase in key VOCs at 24 hours. B) GC-MS TIC of A. fumigatuswith the addition of voriconazole, showing near-complete attenuation inkey VOCs at 24 hours.

FIGS. 10A-B. Positive ion DMS spectra of Aspergillus species, showing A)Conservation of the DMS pattern between two members of A. fumigatus, andB) Conservation of the DMS pattern between two members of A. terreus.The DMS pattern is clearly different between A. fumigatus and A.terreus.

FIGS. 11A-B. Principal component analysis (PCA) score plots for A.fumigatus and A. terreus. 11A) Each letter represents an experimentalreplicate of type strains of A. fumigatus (A) and A. terreus (B).Percentage of total variance and absolute Eigenvalue are outlined inparentheses on each axis. There is clear clustering of A. fumigatus andA. terreus DMS features and separation between these species. 11B) Eachletter represents an experimental replicate of clinical and culturecollection strains of A. fumigatus (A, B) and A. terreus (C, D), withclear clustering within species and distinct separation between species.

FIG. 12. Overlay of the GC-MS total ion chromatograph of arepresentative breath sample of a patient with invasive aspergillosis(black chromatogram) and an in vitro culture of A. fumigatus Af293(inverted red chromatogram).

FIG. 13. This heatmap shows the average integrated area of terpenemetabolites (columns A-H), showing the relative abundance of each key A.fumigatus VOC in the breath of patients with IA and patients without IA.Each row represents an individual patient's breath and each columnrepresents one of the keyA. fumigatus VOCs.

FIG. 14. Attenuation of breath A. fumigatus compounds with antifungaltherapy.

FIG. 15. In Vitro Volatile Organic Compound Profiles of Aspergillusfumigatus and Other Pathogenic Aspergillus Species. Aspergillus specieshave species-specific volatile organic compound profiles, withparticular interspecies heterogeneity in monoterpene and sesquiterpenemetabolites. The following peaks identified as 1) α-pinene; 2) β-pinene;3) Camphene; 4) Limonene; 5) α-trans-bergamotene; 6)β-trans-bergamotene; 7) Elixene; 8) Santalene; 9) Elemene, 10) Acoradien11) 1,5,9-trimethyl-1,5,9-cyclododecatriene; 12) Chamigrene; 13.)β-sesquiphellandrene.

FIGS. 16A-0. Chemical structures and fragmentation patterns of keyterpene Compounds. A) GC-MS spectrum and structure of α-pinene from A.fumigatus; B) GC-MS spectrum and structure of β-pinene from A.fumigatus; C) GC-MS spectrum and structure of camphene from A.fumigatus; D) GC-MS spectrum and structure of limonene from A.fumigatus; E) GC-MS spectrum and structure of trans-α-bergamotene fromA. fumigatus; F) GC-MS spectrum and structure of trans-β-bergamotenefrom A. fumigatus; G) GC-MS spectrum and structure of elixene from A.terreus; H) GC-MS spectrum and structure of santalene from A. terreus;I) GC-MS spectrum and structure of elemene from A. terreus; J) GC-MSspectrum and structure of acoradien from A. terreus; K) GC-MS spectrumand structure of 1,5,9-trimethyl-1,5,9-cyclododecatriene from A.terreus; L) GC-MS spectrum and structure of chamigrene from A. terreus;M) GC-MS spectrum and structure of β-sesquiphellandrene from A.calidoustus; N) GC-MS spectrum and structure of β-vatirenene from breathsamples of patients with A. fumigatus invasive aspergillosis; and O)GC-MS spectrum and structure of trans-geranylacetone from breath samplesof patients with A. fumigatus invasive aspergillosis.

FIGS. 17A-D. Effect of nitrogen starvation, alkaline stress, and irondeprivation stress conditions on the volatile organic compound profileof A. fumigatus Af293. GC-MS analysis of A. fumigatus Af293 cultured for96 hrs in (A) nutrient-rich YPD media, (B) nitrogen starvation, (C)alkaline stress, and (D) iron depletion (McDonagh A, Fedorova N D,Crabtree J, et al. Sub-telomere directed gene expression duringinitiation of invasive aspergillosis. PLoS Pathog. 2008; 4(9):e1000154).Labeled peaks were identified as 1) α-Pinene; 2) β-Pinene; 3) Camphene;4) Limonene; 5) α-trans-bergamotene; 6) β-trans-bergamotene. TIC, totalion count; RT, retention time.

FIGS. 18A-D. Effect of antifungal drug exposure on the volatile organiccompound profile of A. fumigatus Af293 GC-MS analysis of A. fumigatusAf293 after 12 hours of exposure to (A) no antifungal therapy; (B)liposomal amphotericin; (C) micafungin; or (D) voriconazole. Peak 6identified as β-trans-bergamotene. TIC, total ion count; RT, retentiontime.

FIG. 19. In vitro volatile organic compound profiles of Aspergillusflavus and Aspergillus niger. GC-MS analysis of the headspace of 104conidia of A. flavus and A. niger grown for 96 hours in YPD media. Nosesquiterpene metabolites were identified under these growth conditions.TIC, total ion count; RT, retention time.

FIG. 20. Example of changes in volatile peak area over time witheffective antifungal therapy. Response of the A. fumigatus breathmetabolite signature to effective antifungal therapy in a patient withinvasive aspergillosis. Galactomannan EIA, serum galactomannan enzymeimmunoassay index.

DETAILED DESCRIPTION

Pathogenic molds produce VOCs as part of their normal metabolism.Agricultural and environmental health industries have previouslyinvestigated the detection of microbial VOCs to identify spoiled grainand mold-infested ‘sick buildings,’ respectively, and investigators inthese areas have noticed species-specific differences in the compositionof VOCs emitted by molds in these settings.

As described herein, the present inventors have identified unique,species-specific VOC profiles of A. fumigatus, A. terreus, and A.calidoustus in vitro, including several volatile terpene andsesquiterpene compounds that can be used to discriminate these speciesfrom each other and from other molds, and demonstrated that differentialmobility spectrometry (DMS) can be used for the rapid discrimination offungal species using pattern-based identification of thesespecies-specific VOC profiles. The key terpene and sesquiterpenecompounds identified in in vitro cultures of A. fumigatus were alsopresent in the breath of patients with IA, in addition to novelAspergillus VOCs induced in vivo, namely, the sesquiterpenebeta-vatirenene and the oxidized terpene derivativetrans-geranylacetone. A combination of beta-trans-bergamotene,beta-vatirenene, and trans-geranylacetone accurately distinguishedpatients with IA from patients with other causes of pneumonia with 93%sensitivity and 96% specificity.

Detection of these unique VOC profiles can be harnessed forspecies-level identification of Aspergillus and other mold species inthe laboratory, and direct detection of these fungal volatile profilesin the breath of patients with suspected IA can be used for the rapid,noninvasive, highly accurate, and species-specific diagnosis of IA andother fungal pneumonias. The methods and devices described herein, e.g.,the DMS-based detection methods, can be adapted to a small, portablebedside breath gas detection system for real-time patient breathsurveillance for this pattern of fungal metabolites, to allow forearlier IA diagnosis than currently possible, more rational test-basedprescribing of antifungal medications, monitoring of clinical responseto antifungal therapy, and ultimately, better patient outcomes.

As described herein, among other uses, these VOC profiles can be usedfor:

a. rapid, noninvasive, sensitive, and species-specific breath tests forthe diagnosis of invasive aspergillosis and the discrimination ofaspergillosis from other causes of pneumonia in the growing populationof immunocompromised patients at risk for invasive fungal infections;b. surrogate marker demonstrating successful antifungal treatment of IA,andc. rapid identification and antifungal susceptibility testing ofAspergillus species, e.g., in the microbiology laboratory, based ontheir VOC profile (i.e., the VOCs present in the sample).

Invasive Aspergillosis

The methods described herein can be used to detect or diagnose invasiveaspergillosis (IA) in a subject, to select treatment and to treat IA,and to monitor treatment of IA. The methods can be used in the differentforms of invasive aspergillosis, including invasive pulmonaryaspergillosis, sinus or nasal aspergillosis, disseminated aspergillosis,and single-organ invasive aspergillosis, e.g., of an organ in thesino/nasal/respiratory tract (see, e.g., Walsh et al., ClinicalInfectious Diseases 2008; 46:327-60; Milroy et al., J Clin Pathol. 1989February; 42(2): 123-127). In preferred embodiments, the methodsdescribed herein can be used for subjects with invasive pulmonaryaspergillosis.

Samples

The methods described herein can be performed on a gas or liquid sample.In some embodiments, the sample is exhaled breath directly from anindividual or from a breathing machine such as a ventilator.Alternatively, the methods can be performed using headspace from aculture known or suspected to include Aspergillus species, e.g.,commercially-available or lab-cultured species or species obtained froma primary sample from a subject, e.g., a clinical sample obtained bybiopsy of the affected area (e.g., nasal biopsy, transthoracicpercutaneous needle aspiration, or video assisted thoracoscopic biopsy)or bronchoalveolar lavage. The sample is maintained in a suitable growthmedium to allow growth and metabolism of any Aspergillus species in thesample. In certain embodiments, the invention involves taking a clinicalsample from a subject and placing it in media, for example, withmicrofluidics, or in culture, for example, with conventional culturingmethods. The Aspergillus species, if present, are stimulated tometabolize. The headspace (gaseous phase) generated as a result of thismetabolism can be collected and analyzed using a method described hereinor known in the art, see, e.g., US20100291617. In some embodiments, themethods are performed directly on bronchoalveolar washings, obtained bybronchoscopy/bronchoalveolar lavage. In some embodiments, the sample isa gas, e.g., patient breath or gas from the headspace of an in vitroculture sample. Where headspace gas is used, the gas should be collectedafter the headspace has been in contact with the culture for asufficient amount of time for the compounds to be present, preferably inan air-tight, sealed environment.

The VOCs can also be detected in a liquid sample, since they areexpected to be there in equilibrium with the gaseous phase. Thus, inaddition to or as an alternative, the samples assayed using the methodsdescribed herein can include a liquid, e.g., blood (e.g., plasma orserum), lymph, urine, tears, saliva, sputum, nasal mucus, phlegm (e.g.,expectorate), or CSF from a subject (e.g., from a biological fluid thatcomes near or preferably into contact with the tissue or organ that isknown or suspected to be infected with an Aspergillus species), or theliquid phase (e.g., supernatant) of an in vitro culture. In someembodiments, the sample comprises saliva from the subject.

Detection Methods

A number of methods known in the art can be used to detect the presenceof the VOCs described herein in a sample. Exemplary methods(particularly for use with a gas sample) include gas chromatography(GC); spectrometry, for example mass spectrometry (including quadrapole,time of flight, tandem mass spectrometry, ion cyclotron resonance,and/or sector (magnetic and/or electrostatic)), ion mobilityspectrometry, field asymmetric ion mobility spectrometry, and/or DMS;fuel cell electrodes; light absorption spectroscopy; nanoparticletechnology; flexural plate wave (FPW) sensors; electrochemical sensors;photoacoustic equipment; laser-based equipment; electronic noses(bio-derived, surface coated); and various ionization techniques. See,e.g., US20100291617 and US20070003996. Preferred methods include ionmobility spectrometry (IMS) or differential mobility spectrometry (DMS).

In some embodiments, the methods described herein include the use ofdifferential mobility spectrometry to detect VOCs in a sample. Anexemplary micro-machined differential mobility spectrometer (DMS),developed for chemical and biological sensing applications, is currentlyavailable from Sionex Corporation. DMS has several features that make itan excellent platform for VOC analysis: it is quantitative, selective,and exquisitely sensitive, with a volatile detection limit in theparts-per-trillion range (Davis et al., In: 12th InternationalConference on Transducers, Solid-State Sensors, Actuators andMicrosystems; 2003; p. 1233-8 vol. 2; Miller et al., In: Solid-StateSensors and Actuators Workshop; 2000; Hilton Head, S.C.; 2000; Krebs etal., Sensors Journal, IEEE 2005; 5(4):696-703). Unlike massspectrometry, which separates particles based on mass/charge ratios, DMSharnesses differences in ion mobility in low and high electric fields toachieve a gas-phase separation of ions at atmospheric pressure. DMSrapidly detects compounds that are difficult to resolve by otheranalytical techniques such as mass spectrometry in challenging matricessuch as human breath (Kanu et al., J Mass Spectrom 2008; 43:1-22; Kanuet al., J Chromatogr A 2008; 1177:12-27; Luong J et al., J ChromatogrSci 2006; 44:276-286; Nazarov et al., Anal Chem 2006; 7697-706;Kolakowski et al., Analyst 2007; 132:842-64).

DMS can be tuned to monitor specific ion masses, thus tailoring responsecharacteristics to focus on various compounds of interest. It requiresno reagents, generates the high fields required by the sensor using asmall power supply, and has already been microfabricated, resulting in asmall, portable machine that can be used at the bedside, with aturnaround time of several minutes. DMS has been used successfully inseveral commercial settings, including a hand-held, portable detector oftrace levels of chemical warfare agents from General Dynamics (JUNO™)and airport explosives detectors from Thermo (see, e.g., U.S. Pat. No.7,605,367). DMS technology has also been successfully applied to thecharacterization of unique VOCs produced by Mycobacterium tuberculosisand other bacteria (Fong et al., Anal Chem 2011; 83:1537-46; Shnaydermanet al., Anal Chem 2005; 77:5930-7).

To perform a measurement using a DMS, a gas sample is introduced intothe spectrometer, where it is ionized, and the ions are transportedthrough an ion filter towards the detecting electrodes (Faraday plates)by a carrier gas. The DMS device can separate chemical components of asubstance based on differing ion mobilities. For other devices,measurements are performed using methods known in the art.

Additional non-limiting examples of systems that can be used in thepresent methods include those described in US20090078865; US20130168548;US20100291617 and US20070003996.

In some embodiments, the methods include obtaining a sample of ambientair and detecting the presence and/or levels of VOCs in the air, toprovide a reference for subtraction of ambient VOCs.

A number of methods are known in the art for detecting the presenceand/or levels of the VOCs in a liquid sample, including but not limitedto chromatography (e.g., HPLC) and spectrophotometry (e.g., MS, LC-MS,MALDI-TOF, and other of the methods described above for gas-phasesamples).

Combination Diagnostics

In some embodiments, the methods include performing an additionaldiagnostic test for IA. A number of such tests are known in the art andinclude galactomannan enzyme immunoassays; radiology imaging studies(e.g., CT imaging); bronchoalveolar lavage, transthoracic percutaneousneedle aspiration, or video assisted thoracoscopic biopsy. A positiveresult on one of these tests can provide further evidence supporting adiagnosis of IA; see, e.g., Walsh et al., Clinical Infectious Diseases2008; 46:327-60.

Aspergillus Species Identification and Diagnosis

As described herein, A. fumigatus, A. terreus, A. calidoustus eachproduce VOCs that can be used to identify them in a sample, e.g., in asample comprising breath of a subject, or headspace from a culturesuspected of comprising Aspergillus; the culture can be, e.g., a cultureof a biopsy from a subject, or a culture in a microbiology laboratory,e.g., a culture known or suspected of containing or being contaminatedwith an Aspergillus species. This identification can be used to diagnosea subject with the specific species of Aspergillus, allowing for theadministration of species-specific treatments, e.g., as described below.

Thus, the methods described herein can include obtaining a samplecomprising breath of a subject, or headspace from a culture suspected ofcomprising Aspergillus, and detecting and identifying the VOCs in thesample. For example, the methods can include detecting the presence ofone, two, three, or more, e.g., all, of camphene, alpha-pinene,beta-pinene, limonene, alpha-bergamotene, beta-trans-bergamotene,elixene, alpha-santalene, beta-elemene, acoradien, chamigrene,1,5,9-trimethyl cyclododecatriene, 9-decene-2-one andbeta-sesquiphellandrene in the sample. The presence of one, two, three,or more, e.g., all, of camphene, alpha-pinene, beta-pinene, limonene,alpha-bergamotene, or beta-trans-bergamotene indicates the presence ofA. fumigatus in the sample (and thus an A. fumigatus infection in caseswhere the sample is from a subject); the presence of one, two, three, ormore, e.g., all, of elixene, alpha-santalene, beta-elemene, acoradien,chamigrene, and 1,5,9-trimethyl cyclododecatriene indicates the presenceof A. terreus in the sample (and thus an A. terreus infection in caseswhere the sample is from a subject); and the presence of one or both of9-decene-2-one and beta-sesquiphellandrene indicates the presence of A.calidoustus in the sample (and thus an A. calidoustus infection in caseswhere the sample is from a subject). In some embodiments, where limoneneor alpha-pinene is present, at least one or two other VOCs must also bepresent for a positive species identification, and a species-specificdiagnosis, to be made.

Methods of Treatment

The methods described herein can be used to select a treatment for asubject, and can optionally include administering the treatment to asubject. When a subject has been diagnosed by a method described hereinas having IA, then a treatment comprising administration of atherapeutically effective amount of an antifungal compound can beadministered.

A number of antifungal compounds are known in the art and underdevelopment. At present, deoxycholate amphotericin B (D-AMB) and itslipid formulations (AMB lipid complex (ABLC), liposomal amphotericin B(LAMB), and Amphotericin B cholesteryl sulfate complex (AMB colloidaldispersion, ABCD)); azole compounds (itraconazole, voriconazole,posaconazole); and echinocandins (caspofungin, micafungin,anidulafungin) are in clinical use, though voriconazole and D-AMB arethe only compounds approved for primary treatment of invasiveaspergillosis in the United States. For detailed information ontreatment of IA, see, e.g., Walsh et al., Clinical Infectious Diseases2008; 46:327-60; and Man et al., Treatment and prevention of invasiveaspergillosis, Up-To-Date (topic updated on Oct. 18, 2012; literaturereview August 2013; available atuptodate.com/contents/treatment-and-prevention-of-invasive-aspergillosis?topicKey=ID%2F2459&elapsedTimeMs=7&view=print&displayedView=full).

In some embodiments, the methods include selecting and optionallyadministering an azole antifungal, e.g., itraconazole (ITR),voriconazole (VOR), posaconazole (POS), ravuconazole (RAV), orisavuconazole (ISA), or an amphotericin B (AMB) formulation as describedabove, to a subject identified by a method described herein as havingIA. In some embodiments, the methods include administering anechinocandin, e.g., caspofungin, micafungin or anidulafungin, e.g.,alone or in combination with an azole (e.g., voriconazole) or AMB.

It is known that triazoles are not active against some isolates of A.calidoustus, and some A. terreus isolates are resistant to AMB. See,e.g., Baddley et al., J. Clin. Microbiol. 2009, 47(10):3271. Thus, insome embodiments, where the species of Aspergillus is determined, anazole compound (e.g., ITR, VOR, POS, RAV, or ISA) is selected for (andoptionally administered to) a subject who has A. fumigatus or A.terreus, but not A. calidoustus. In some embodiments, an AMB (e.g.,D-AMB, ABLC, LAMB, or ABCD) is selected for (and optionally administeredto) a subject who has A. calidoustus. In some embodiments, an AMB isselected for (and optionally administered to) a subject who has A.fumigatus, but not a subject who has A. terreus.

In some embodiments, the methods described herein can be used todetermine susceptibility of Aspergillus species, e.g., to treatment witha known or suspected antifungal, e.g., in the microbiology laboratory. Asample suspected or known to include Aspergillus from a subject isobtained and cultured as described above, e.g., under conditionsmimicking the in vivo environment, and then exposed to a potentialtreatment (e.g., a known or experimental treatment). After exposure tothe treatment, the VOCs present in the headspace of the culture aresampled. If the treatment decreases VOCs as compared to a referencelevel (e.g., a level of VOCs in the headspace before exposure to thetreatment), then the Aspergillus in the sample is considered susceptibleto the treatment. In this case, the treatment is likely to be effectivein treating IA in the subject; the treatment can be selected andoptionally administered to subject.

Monitoring Treatment Efficacy

As described herein, successful treatment of an Aspergillus infectionresults in a decrease in fungal VOCs. Thus, the methods can includerepeated assays of VOC levels in a subject, e.g., before, during, andafter administration of a treatment for IA. A decrease in VOC levelswould indicate that the treatment has been successful. In someembodiments, levels of one, two, or all three of beta-trans-bergamotene,beta-vatirenene, and/or trans-geranylacetone are determined. In someembodiments, levels of one, two, three, or more ofbeta-trans-bergamotene, beta-vatirenene, trans-geranylacetone, camphene,alpha-pinene, beta-pinene, limonene, alpha-bergamotene,beta-trans-bergamotene, elixene, alpha-santalene, beta-elemene,acoradien, chamigrene, 1,5,9-trimethyl cyclododecatriene, 9-decene-2-oneand beta-sesquiphellandrene are determined.

Methods of Identifying Novel Antifungal Agents

Included herein are methods for screening test compounds, e.g.,polypeptides, polynucleotides, inorganic or organic large or smallmolecule test compounds, to identify agents useful in the treatment ofIA.

As used herein, “small molecules” refers to small organic or inorganicmolecules of molecular weight below about 3,000 Daltons. In general,small molecules useful for the invention have a molecular weight of lessthan 3,000 Daltons (Da). The small molecules can be, e.g., from at leastabout 100 Da to about 3,000 Da (e.g., between about 100 to about 3,000Da, about 100 to about 2500 Da, about 100 to about 2,000 Da, about 100to about 1,750 Da, about 100 to about 1,500 Da, about 100 to about 1,250Da, about 100 to about 1,000 Da, about 100 to about 750 Da, about 100 toabout 500 Da, about 200 to about 1500, about 500 to about 1000, about300 to about 1000 Da, or about 100 to about 250 Da).

The test compounds can be, e.g., natural products or members of acombinatorial chemistry library. A set of diverse molecules should beused to cover a variety of functions such as charge, aromaticity,hydrogen bonding, flexibility, size, length of side chain,hydrophobicity, and rigidity. Combinatorial techniques suitable forsynthesizing small molecules are known in the art, e.g., as exemplifiedby Obrecht and Villalgordo, Solid-Supported Combinatorial and ParallelSynthesis of Small-Molecular-Weight Compound Libraries,Pergamon-Elsevier Science Limited (1998), and include those such as the“split and pool” or “parallel” synthesis techniques, solid-phase andsolution-phase techniques, and encoding techniques (see, for example,Czarnik, Curr. Opin. Chem. Bio. 1:60-6 (1997)). In addition, a number ofsmall molecule libraries are commercially available. A number ofsuitable small molecule test compounds are listed in U.S. Pat. No.6,503,713, incorporated herein by reference in its entirety.

Libraries screened using the methods of the present invention cancomprise a variety of types of test compounds. A given library cancomprise a set of structurally related or unrelated test compounds. Insome embodiments, the test compounds are peptide or peptidomimeticmolecules. In some embodiments, the test compounds are nucleic acids.

In some embodiments, the test compounds and libraries thereof can beobtained by systematically altering the structure of a first testcompound, e.g., a first test compound that is structurally similar to aknown natural binding partner of the target polypeptide, or a firstsmall molecule identified as capable of binding the target polypeptide,e.g., using methods known in the art or the methods described herein,and correlating that structure to a resulting biological activity, e.g.,a structure-activity relationship study. As one of skill in the art willappreciate, there are a variety of standard methods for creating such astructure-activity relationship. Thus, in some instances, the work maybe largely empirical, and in others, the three-dimensional structure ofan endogenous polypeptide or portion thereof can be used as a startingpoint for the rational design of a small molecule compound or compounds.For example, in one embodiment, a general library of small molecules isscreened, e.g., using the methods described herein.

In some embodiments, a test compound is applied to a test samplecomprising one or more Aspergillus species, and the ability of the testcompound to decrease levels of a VOC as described herein in theheadspace of the culture is determined.

In some embodiments, the test sample is, or is derived from (e.g., asample taken from) an in vivo model of a disorder as described herein.For example, an animal model, e.g., a rodent (such as a rat or mouse)that has been infected with one or more Aspergillus species can be used.

A test compound that has been screened by a method described herein anddetermined to decrease VOCs, can be considered a candidate compound. Acandidate compound that has been screened, e.g., in an in vivo model ofa disorder, e.g., a rodent infected with one or more Aspergillusspecies, and determined to decrease VOCs in a sample comprising breathfrom the infected animal model or headspace from a culture of a samplefrom the infected animal model, can be considered a candidatetherapeutic agent. Candidate therapeutic agents, once screened in aclinical setting, are therapeutic agents. Candidate compounds, candidatetherapeutic agents, and therapeutic agents can be optionally optimizedand/or derivatized, and formulated with physiologically acceptableexcipients to form pharmaceutical compositions. Thus, test compoundsidentified as “hits” (e.g., test compounds that decrease fungal VOCs inan animal model) in a first screen can be selected and systematicallyaltered, e.g., using rational design, to optimize binding affinity,avidity, specificity, or other parameter. Such optimization can also bescreened for using the methods described herein. Thus, in oneembodiment, the invention includes screening a first library ofcompounds using a method known in the art and/or described herein,identifying one or more hits in that library, subjecting those hits tosystematic structural alteration to create a second library of compoundsstructurally related to the hit, and screening the second library usingthe methods described herein.

Test compounds identified as hits can be considered candidatetherapeutic compounds, useful in treating IA. A variety of techniquesuseful for determining the structures of “hits” can be used in themethods described herein, e.g., NMR, mass spectrometry, gaschromatography equipped with electron capture detectors, fluorescenceand absorption spectroscopy. Thus, the invention also includes compoundsidentified as “hits” by the methods described herein, and methods fortheir administration and use in the treatment, prevention, or delay ofdevelopment or progression of a disorder described herein.

Test compounds identified as candidate therapeutic compounds can befurther screened by administration to an animal model of IA, asdescribed herein. The animal can be monitored for a change in thedisorder, e.g., for an improvement in a parameter of the disorder, e.g.,a parameter related to clinical outcome. In some embodiments, theparameter is VOCs or survival, and an improvement would be a reductionin VOCs or an increase in survival. In some embodiments, the subject isa human, e.g., a human with IA and the parameter is levels of fungalVOCs or survival.

Examples

The invention is further described in the following examples, which donot limit the scope of the invention described in the claims.

Example 1. Definition of Aspergillus VOC Profiles In Vitro

Using gas chromatography interfaced to mass spectrometry anddifferential mobility spectrometry (GC-MS/DMS), VOC profiles werecharacterized in the headspace gas of in vitro cultures of Aspergillusspecies pathogenic to humans, most notably A. fumigatus, A. terreus, andA. calidoustus, under incubation conditions designed to mimic the milieuof the human lung and promote hyphal growth (as Aspergillus spreadsthrough hyphal growth and invasion of human tissue blood vessels andtissues in vivo).

Mold strains (Table A) were incubated at 25° C. on Sabouraud dextroseagar slants. Conidia were harvested and conidial suspensions wereprepared in sterile water. Conidia were quantified with a hemocytometer.

TABLE A Fungal species used for in vitro VOC profile determinationStrains Genus Species (N) Source* Aspergillus fumigatus 9 ATCC, CDC, BWHAspergillus terreus 7 ATCC, BWH Aspergillus calidoustus 3 ATCCAspergillus niger 6 CDC, BWH Aspergillus tubingensis 2 CDC Aspergillusflavus 5 CDC, BWH Rhizopus oryzae 3 ATCC, BWH Fusarium solani 2 ATCC,BWH Mucor velutinosus 1 BWH *ATCC: American Type Culture Collection,CDC: Centers for Disease Control; BWH: Brigham and Women's Hospital

For each experiment, 10⁴ conidia were inoculated into 5 mL of microbialmedia (either nutrient Yeast Extract Peptone Dextrose (YPD) broth,nutrient poor Aspergillus minimal media (Pontecorvo et al., Advan Genet1953; 5:141-238), or under iron-starved, alkaline stress, ornitrogen-depleted conditions (McDonagh et al., PLoS Pathog 2008;4:e1000154)) in 20 mL glass vials with an airtight crimp topincorporating a rubber septum. Cultures were incubated for 24-144 hoursat 200 rpm and 37° C. and headspace gas was dynamically adsorbed, usingargon carrier gas and an air sampling pump calibrated to 20 mL/minute,onto Markes thermal desorption traps containing tandem beds of Tenax TA(200 mg), Carbograph 1 TD (100 mg), and Carboxen 1003 (100 mg),optimized to retain VOCs of diverse size and polarity.

Headspace VOCs were also collected after exposure of a subset of fungalisolates to the antifungal drugs voriconazole, liposomal amphotericin B,and micafungin, each at a concentration of 1.0 mg/mL.

VOCs were desorbed onto a dual GC-MS/DMS system (FIG. 1)—the eluent fromthe gas chromatograph was split between the MS, to allow identificationof each compound, and the DMS, an extremely sensitive and selective gasdetector that can be easily used as a point-of-care gas detectiondevice, to determine the mobility pattern for each compound. The NIST MSSearch 2.0 Library was used to identify VOCs in the total ionchromatogram (TIC) of the GC-MS data. Differences in spectral featuresof DMS output were visually distinguished between the positive ionspectra of A. fumigatus and A. terreus and principal component analysis(PCA) was used to evaluate the degree of class discrimination betweenthese fungal species using algorithms in MATLAB (Version R2012a).

Collection of VOCs in Patient Breath

Breath was collected from patients with suspected IA using a LoccioniBreath Analysis sampler. For each patient, up to 4 minutes of tidalbreath was adsorbed using an an air sampling pump calibrated to 900mL/minute onto two parallel thermal desorption traps containing tandembeds of Tenax TA (200 mg), Carbograph 1 TD (100 mg), and Carboxen 1003(100 mg). Ambient air was sampled concurrently with each breath sampleat a flow rate of 900 mL per minute to control for any environmentalVOCs in patient breath samples. These samples were analyzed using thesame thermal desorption GC-MS method outlined above for the in vitrofungal cultures.

Results

Intraspecies Homogeneity, Interspecies Heterogeneity of VOC Profiles:

Each mold species tested in vitro produced a distinctive VOC profilethat was conserved within each species (FIG. 2A) and distinct betweenspecies (FIG. 2B). Terpene and sesquiterpene compounds were particularlydistinct between different fungal species.

Comparison of the VOC profile of A. fumigatus with other fungal speciesshowed that camphene, alpha-pinene, beta-pinene, limonene,alpha-bergamotene, and beta-trans-bergamotene were characteristic of A.fumigatus (FIG. 3). Comparison of the VOC profile of A. terreus withother fungal species showed that elixene, alpha-santalene, beta-elemene,acoradien, chamigrene, and 1,5,9-trimethyl cyclododecatriene were keyfeatures characteristic of A. terreus (FIG. 4). Comparison of the VOCprofile of A. calidoustus with other fungal species showed that9-decene-2-one and beta-sesquiphellandrene were key VOC featurescharacteristic of A. calidoustus (FIG. 5).

Kinetics of VOC Production In Vitro:

The kinetics of VOC release were assessed in vitro over lag, log,stationary, and death phases of each mold species, over 24-144 hours ofincubation at 37° C. The key VOC features of A. fumigatus were firstclearly discernible at 24 hours of incubation and all volatiles reachedtheir peak concentration at 96 hours of incubation (FIG. 6).

The key VOC features of A. terreus were first clearly discernible at 48hours of incubation and reached peak levels at 96-120 hours ofincubation (FIG. 7).

The key VOC features of A. calidoustus were first clearly discernible at24-48 hours of incubation and reached their peak at 96 hours ofincubation (FIG. 8).

Antifungal Exposure Modulates the Release of VOCs in A. fumigatus:

Whether exposure to antifungal drugs might modulate VOC release inAspergillus fumigatus was assessed in vitro. When micafungin was addedto 48-hour hyphal cultures of A. fumigatus, up to a 17-fold increase insome of the key A. fumigatus VOC features was observed after 24 hours,compared to matched control samples without micafungin (FIG. 9A);attenuation of these VOC features was observed with a longer duration ofincubation and hyphal death. A similar initial increase then attenuationin key A. fumigatus VOCs was observed in response to liposomalamphotericin B. When voriconazole was added to 48-hour hyphal culturesof A. fumigatus, near-complete attenuation of the key VOC features ofthis species was observed after 24 hours, compared to matched controlsamples without voriconazole (FIG. 9B).

Definition of GC-Differential Mobility Spectrometer Patterns of A.fumigatus and A. terreus:

As a step towards utilizing portable GC-differential mobilityspectrometry (DMS) technology as a point-of-care gas detector forAspergillus, the eluent from the GC was split between a MS and a DMSdevice. DMS is an extremely sensitive and selective chemical detectorthat operates at atmospheric pressure with a small power source,allowing it to be used outside the laboratory for the detection ofspecific VOC patterns. DMS positive ion spectral features of headspacegas from A. fumigatus and A. terreus were examined. The DMS pattern wasclearly conserved within members of each species and clearly distinctbetween A. fumigatus and A. terreus (FIG. 10A, 10B).

Using principal component analysis (PCA), the degree of class separationbetween A. fumigatus and A. terreus was evaluated. There was clusteringof samples from the same species, and clear separation between A.fumigatus and A. terreus clusters (FIG. 11A, 11B).

Detection of A. fumigatus VOCs in Patient Breath:

Tidal breath was collected from 54 immunocompromised patients withsuspected invasive aspergillosis to assess whether patients with IAcould be distinguished from patients without IA by detecting fungal VOCsin their breath.

Of 54 patients, 23 (43%) were female, 46 (85%) had a hematologicmalignancy, 22 (41%) allogeneic stem cell transplants, 6 (11%) solidorgan transplants, 46 (85%) exposure to T-cell immunosuppressants, and24 (44%) prolonged neutropenia. These characteristics were comparable in29 patients with EORTC/MSG proven (3) or probable (26) IA and 25patients with nodular pneumonia caused by other fungal infections orother infectious processes.

There was substantial overlap between the key A. fumigatus VOCs weidentified in vitro and in the breath of patients with invasiveaspergillosis (FIG. 12), although we also identified a new sesquiterpenecompound, beta-vatirenene, and an oxidized terpene derivative,trans-geranylacetone, in the breath of patients with IA that were notinduced by any of our in vitro culture conditions.

While some of the key VOCs identified in A. fumigatus in vitro werepresent equally in patients with and without IA, a combination ofbeta-trans-bergamotene and beta-vatirenene and the oxidized terpenederivative trans-geranylacetone distinguished patients with IA frompatients without IA correctly in 51/54 (94%) patients (FIG. 13)—27 of 29patients with IA (sensitivity=93%) and 24 or 25 patients who ultimatelyhad other causes of pneumonia (sensitivity=96%). These VOCs were absentin ambient air control samples collected concurrently with each breathsample.

Breath was collected from a few patients serially following initiationof antifungal therapy and these key A. fumigatus VOCs appeared todecline over 1-2 weeks of treatment.

Example 2. A Breath Fungal Secondary Metabolite Signature to DiagnoseInvasive Aspergillosis

Objective:

To define the volatile metabolic profile of Aspergillus fumigatus, themost common cause of invasive aspergillosis, and assess whether patientswith invasive aspergillosis can be distinguished from patients withother pneumonia by direct detection of fungal metabolites in theirbreath.

Design:

The study had two parts: A) An in vitro assessment of the volatilemetabolite profile of pathogenic Aspergillus species, and B) Prospectivecollection of breath samples from individuals with suspected invasiveaspergillosis from 2011-2013, with measurement of volatile metabolitesof fungal origin using thermal desorption-gas chromatography/massspectrometry.

Methods

Aspergillus Isolates:

We characterized the in vitro VOC profile of the most common cause ofIA, Aspergillus fumigatus (A. fumigatus Af293, A. fumigatus A1163, and 7invasive clinical isolates). For comparison, we also investigated the invitro VOC profiles of A. terreus, A. flavus, A. niger, and A.calidoustus, an emerging Aspergillus species with in vitro resistance totriazole antifungal drugs.^(24, 25) Specific strains are listed online(Methods). The species identity of all strains was confirmed by ITS andβ-tubulin sequencing at the Fungus Testing Laboratory at the Universityof Texas Health Science Center at San Antonio or at the Centers forDisease Control (CDC).²⁶

Fungal Culture and Headspace Extraction Conditions:

Conidial suspensions were prepared in sterile water for each Aspergillusisolate. 10⁴ A. fumigatus conidia were inoculated into 5 mL of variousliquid media in a 20 mL glass vial sealed with an airtight capincorporating a silicone septum (Restek Corporation, Bellefonte, Pa.),with concurrent media controls. We used a range of liquid media, giventhe potential for substrate-dependent secondary metaboliteproduction²⁷—yeast extract-peptone-dextrose (YPD) broth (Teknova,Hollister, Calif.), Aspergillus minimal media,²⁸ and culture conditionsthat have been shown to generate A. fumigatus transcriptomes in vitrothat overlap with its transcriptome in a murine lung infection model,including iron-limited, nitrogen depleted, and alkaline stressconditions²¹—in sets of 4 technical replicates for each A. fumigatusisolate. Each vial was incubated in an orbital shaker at 250 rpm topromote hyphal, rather than conidial, growth at 37° C. for 96 hours.Headspace gas in each vial was dynamically adsorbed over 2 minutes persample, using argon carrier gas and an air sampling pump calibrated to20 mL per minute, onto thermal desorption tubes containing tandemsorbent beds of Tenax TA (200 mg), Carbograph 1 TD (100 mg), andCarboxen 1003 (100 mg) (Markes International, Llantrisant, UnitedKingdom), to retain polar and nonpolar VOCs over a wide range of boilingpoints.

We assessed whether we could modulate the A. fumigatus VOC metabolomewith voriconazole, micafungin, and liposomal amphotericin B antifungaldrug exposure, as described online (Methods). Headspace volatilemetabolites of A. terreus, A. flavus, A. niger, and A. calidoustus werecharacterized as outlined above, in YPD broth at 96 hours.

Patients and Study Procedures:

Adult patients at Brigham and Women's Hospital and Dana-Farber CancerInstitute with suspected pulmonary IA, based on host risk factors,clinical symptoms, and radiologic findings suggestive of invasive fungaldisease (IFD), were eligible for this breath collection study fromNovember 2011 to September 2013. We were notified of patients withsuspected IFD by inpatient and ambulatory oncology, transplant, andimmunocompromised host infectious diseases care teams. Exclusioncriteria were technical inability to provide a tidal breath sample andreceipt of mechanical ventilation. Study participants provided writteninformed consent. Sixty-five of 67 consecutive individuals approachedfor this study provided written informed consent. One patient developedthe acute onset of mental status changes shortly after providinginformed consent and was unable to participate. This study was approvedby the Partners Human Research Committee and the Office for HumanResearch Studies at the Dana-Farber Cancer Institute.

We prospectively collected tidal breath samples from each patient usinga Programmable Breath Sampler (Gruppo Loccioni, Ancona, Italy), whichdisplays real-time measurements of carbon dioxide and mouth pressure,allowing reproducibility of breathing patterns in each patient. Wesampled four minutes of tidal breathing, with dynamic adsorption ofbreath VOCs using an air sampling pump calibrated to 900 mL per minuteover the 4 minute period. Breath VOCs were adsorbed onto two parallelthermal desorption tubes made to the same specifications as the tubes weused for the in vitro experiments. Two samples of ambient air from eachpatient's inpatient or ambulatory room were collected concurrently witheach breath sample using identical air sampling pump and thermaldesorption tube parameters, to assess for environmental volatiles.

In addition to prospective collection of data on patient demographicsand host, clinical, and mycology data required for an assessment of thelikelihood of invasive fungal disease (IFD) in each patient, we recordedfactors that might potentially cause spurious signals in each patient'sbreath VOC profile, including the time and contents of the last mealprior to breath sampling, tobacco use, and details of concurrentmedication exposure.

Patients were classified as having ‘proven,’ probable,′ or ‘possible’IFD independently by two experts (SK and FMM) blinded to the volatileassessment, according to the revised European Organization for Researchand Treatment of Cancer/Mycoses Study Group (EORTC/MSG) consensuscriteria,²⁹ the current gold standard for diagnostic classification ofpatients with IFD. This assessment was performed ≧1 month after initialbreath collection. Patients with ‘proven’ or ‘probable’ aspergillosiswere considered true IA cases for the reference standard, while patientswith ‘possible’ IFD or other fungal causes of ‘proven’ or ‘probable’ IFDwere considered non-IA cases.

Thermal Desorption/Gas Chromatography-Mass Spectrometry:

For both in vitro culture headspace extractions and patient breathsamples, VOCs were thermally desorbed using an automated thermaldesorption unit interfaced to a gas chromatograph (GC)-mass spectrometer(MS), as outlined online (Methods).

Spectral Data Analysis:

We used the National Institute of Standards and Technology (NIST) 11Mass Spectral Library (Scientific Instrument Services, Ringoes, N.J.)for provisional identification of each GC-MS peak in the total ionchromatogram of each in vitro culture, breath sample, and media orambient air control. Analysis of VOCs in breath samples, includingprovisional identification of peaks and analysis of the integrated areaof each peak, was performed by HRT and SDD without knowledge of patientIA status. The chemical identity of monoterpene and sesquiterpene peakswas verified with pure chemical standards of each key peak, whereavailable, or against essential oils containing these compounds, asdetailed online (Methods).

Statistical Analysis:

We used a Bayesian approach to the analysis of patient breath data,focusing on distinctive sesquiterpene volatile metabolites identified inthe headspace of in vitro A. fumigatus cultures, and their derivatives.As we hypothesized a priori based on our in vitro experiments that thesedistinctive A. fumigatus VOCs would be entirely absent in individualswithout IA, we assessed for the qualitative presence or absence of anyof these volatile elements in each individual breath sample. We used theheatmap.2 function in the R gplots package³⁰ to plot the relativeabundance of monoterpene and sesquiterpene metabolites and relatedcompounds in the first breath of each study patient. We used theMann-Whitney test and Fisher's exact test to assess the null hypothesisof no difference in clinical covariates between patients with IA andpatients without IA and calculated two-tailed p-values. We calculatedthe sensitivity and specificity of A. fumigatus VOC metabolite signaturefor IA with exact binomial 95% confidence intervals (CI). We calculatedpositive and negative likelihood ratios and corresponding 95% CI.³¹ Weused Stata 11 (StataCorp LP, College Station, Tex.) for these analyses.

List of Aspergillus Isolates Characterized In Vitro:

We characterized the in vitro VOC profile of the most common cause ofIA, Aspergillus fumigatus (A. fumigatus Af293, A. fumigatus A1163, and 7invasive clinical isolates). For comparison, we also investigated the invitro VOC profiles of A. terreus (A. terreus 601.65 (the type strain ofA. terreus var. terreus) and 6 invasive clinical isolates from theTransplant-Associated Infection Surveillance Network [TRANSNET] (BalajeeS A, Kano R, Baddley J W, et al. Molecular identification of Aspergillusspecies collected for the Transplant-Associated Infection SurveillanceNetwork. J Clin Microbiol. 2009; 47(10):3138-3141)), A. flavus, A. niger(6 invasive clinical isolates each from TRANSNET), and an emergingAspergillus species with in vitro resistance to triazole antifungaldrugs, A. calidoustus (A. calidoustus 121601 (the holotype of A.calidoustus), and 2 invasive clinical isolates from TRANSNET) (Varga J,Houbraken J, Van Der Lee H A L, Verweij P E, Samson R A. Aspergilluscalidoustus sp. nov., causative agent of human infections previouslyassigned to Aspergillus ustus. Eukaryot Cell. 2008; 7(4):630-638;Baddley J W, Marr Ka, Andes D R, et al. Patterns of susceptibility ofAspergillus isolates recovered from patients enrolled in theTransplant-Associated Infection Surveillance Network. J Clin Microbiol.2009; 47(10):3271-3275).

Assessment of the A. fumigatus Volatome Response to Antifungal DrugExposure:

For an assessment of A. fumigatus VOC response to antifungal drugexposure, 10⁴ A. fumigatus Af293 and A1163 conidia were inoculated intoYPD broth and incubated at 37° C. at 250 rpm for 48 hours, then exposedto an inhibitory dose (1.0 μg/mL) of voriconazole (Pfizer Inc., NewYork, N.Y.), micafungin, liposomal amphotericin (both Astellas PharmaUS, Inc., Northbrook, Ill.), or no antifungal therapy for 12 hours, in 4technical replicates, with matched media controls exposed to the sameconditions. VOCs in the headspace of each vial were extracted ontothermal desorption tubes. The cultures and media samples were incubatedat 37° C. at 250 rpm for another 36 hours, with repeat extraction of theheadspace gas onto thermal desorption tubes.

Thermal Desorption/Gas Chromatography-Mass Spectrometry Parameters:

After breath sampling, sorbent traps were sealed with airtight metalcaps with Teflon ferrules (Swagelok, Solon, Ohio) and stored at 4° C.until thermal desorption. Most sorbent traps were desorbed within a fewhours of patient breath sampling, although some sorbent traps werestored for up to one week before thermal desorption without appreciableloss of signal.

For both in vitro culture headspace extractions and patient breathsamples, VOCs were thermally desorbed onto an automated thermaldesorption unit (TD-100, Markes International) at 290° C. for 20 minuteswith helium carrier gas at a flow rate of 40 mL per minute andconcentrated onto a Unity2/TD-100 cold trap (U-15ATA-2S, MarkesInternational). The cold trap was rapidly heated to 270° C. to deliveradsorbed VOCs (3.5:1 split) to a VF624 capillary column (30m×0.32 mm, 6%cyanopropyl/phenyl, 94% polydimethylsiloxane, film thickness 1.8 μm,Agilent Technologies, Santa Clara, Calif.) with a gas chromatograph (GC)inlet temperature of 250° C. VOCs delivered to the capillary column wereseparated using a GC temperature program of 40° C. for 3 minutes, raisedto 70° C. at a rate of 5° C. per minute and held for 3 minutes, raisedto 203° C. at 7° C. per minute and held for 4 minutes, then rapidlyraised to 270° C. and held for 5 minutes. A single quadrupole massspectrometry (MS) detector (Agilent 5975, Agilent Technologies, SantaClara, Calif.) was used to analyze and identify VOCs, with a MS sourcetemperature of 230° C., MS quad temperature of 150° C., and an electronionization parameter of 1412 eV. A mass range m/z 40-400 was measuredwith a threshold of 150.

Confirmation of Compound Identity:

We used the National Institute of Standards and Technology (NIST) 11Mass Spectral Library (Scientific Instrument Services, Ringoes, N.J.)for provisional identification of GC-MS peaks in the total ionchromatogram of each culture, breath sample, and media or ambient aircontrol.

The chemical identity of monoterpene and sesquiterpene peaks wasverified by spiking pure chemical standards of each key peak (α- andβ-pinene, limonene, camphene (all Sigma-Aldrich, St. Louis, Mo.), andβ-trans-bergamotene (gift of Drs. Hsiao-Ching Lin and Yi Tang; Lin H-C,Chooi Y-H, Dhingra S, Xu W, Calvo A M, Tang Y. The fumagillinbiosynthetic gene cluster in Aspergillus fumigatus encodes a crypticterpene cyclase involved in the formation of β-trans-bergamotene. J AmChem Soc. 2013; 135(12):4616-4619)) in 96-hour A. fumigatus cultures,with confirmation of augmentation of our provisionally identified peakcompared to an unspiked culture and a matching fragmentation pattern.The chemical identity of α-trans-bergamotene was confirmed by GC-MSanalysis of bergamot oil (Sigma-Aldrich, St. Louis, Mo.), with retentiontime and fragmentation pattern matching between our provisionallyidentified peak and α-trans-bergamotene in the essential oil. Theidentity of trans-geranylacetone was confirmed by GC-MS analysis of ageranylacetone standard (Sigma-Aldrich, St. Louis, Mo.), with spectraland retention time matching to our compound. We attempted to confirm theidentity of the breath sesquiterpene metabolite identified by the NISTlibrary as β-vatirenene by GC-MS analysis of vetivert essential oil(Nature's Alchemy, Twin Lakes, Wis.) (Chou S-T, Lai C-P, Lin C-C, ShihY. Study of the chemical composition, antioxidant activity andanti-inflammatory activity of essential oil from Vetiveria zizanioides.Food Chem. 2012; 134(1):262-268).

Results

In Vitro VOC Profile of Aspergillus fumigatus:

The volatile monoterpene secondary metabolites camphene, α-pinene,β-pinene, and limonene, and sesquiterpene metabolitesα-trans-bergamotene and β-trans-bergamotene were distinctive andprominent features of A. fumigatus (FIGS. 15 and 16A-O), consistent inall biologic replicates of A. fumigatus. Growth in Aspergillus minimalmedia or under iron-limited, nitrogen depleted, or alkaline stressconditions did not induce the production of any new VOCs. Iron-limitedconditions attenuated monoterpene and sesquiterpene production, whilenitrogen starvation and alkaline stress enhanced β-trans-bergamoteneproduction (FIGS. 17A-D).

Exposure of A. fumigatus hyphae to antifungal drugs modulated VOCproduction, particularly sesquiterpenes: β-trans-bergamotene increased10-fold from baseline with 12 hours of micafungin exposure, and 3-foldwith 12 hours of liposomal amphotericin exposure, followed bynear-complete attenuation of all volatile metabolites 36 hours later. Invitro voriconazole exposure, in contrast, reduced primary metabolite,monoterpene, and sesquiterpene production at 12 hours, with attenuationof all volatile metabolites 36 hours later (FIGS. 18A-D).

Distinct VOC Profiles of Other Aspergillus Species:

Each Aspergillus species we tested had a species-specific VOC profile,consistent within biological replicates of each species and distinctbetween species, with particular interspecies heterogeneity inmonoterpene and sesquiterpene metabolites (FIG. 15). A. terreus (FIGS.15 and 16A-O) had a particularly rich and abundant profile ofsesquiterpene secondary metabolites, and A. calidoustus (FIGS. 15 and16A-O) consistently produced β-sesquiphellandrene. Under these cultureconditions, A. flavus and A. niger produced alcohols and ketones inabundance, but no volatile secondary metabolites other than limonene(FIG. 19). Other than limonene, there was no monoterpene orsesquiterpene overlap between A. fumigatus and any of the otherpathogenic Aspergilli assessed.

A Volatile A. fumigatus-Specific Secondary Metabolite Signature in theBreath of Patients with Invasive Aspergillosis:

Of 64 consecutive patients with suspected IFD, comprising aheterogeneous group of patients with underlying hematologic malignancy,allogeneic hematopoietic stem-cell transplantation, and solid organtransplantation (Table 1), 34 were ultimately diagnosed with IA and 30with other types of pneumonia, including other IFD (Table 2). Mostpatients had received empiric or prophylactic mold-active antifungaltherapy for a median of 2 days prior to breath sampling (Table 1). Therewere no adverse events related to the breath collection procedure.

TABLE 1 Patient Characteristics Invasive Other Aspergillosis Pneumoniap- Clinical Variable (N = 34) (N = 30) value Median age, years (IQR;range) 55 (47, 62; 54 (44, 63; 0.92 22, 79) 28, 87) Female gender, N (%)17 (50%) 8 (27%) 0.07 Hematologic malignancy, N (%) 29 (85%) 24 (80%)0.74 Allogeneic hematopoietic stem-cell 18 (53%) 7 (27%) 0.02transplantation, N (%) Solid organ transplantation, N (%) 3 (9%) 5 (17%)0.46 Recent neutropenia*, N (%) 13 (38%) 15 (50%) 0.45 T-cellimmunosuppressants^(†), N (%) 29 (85%) 26 (87%) 0.58 Prolongedcorticosteroid 7 (21%) 5 (17%) 0.45 exposure^(‡), N (%) Exposure tomold-active antifungal 25 (74%) 26 (87%) 0.23 therapy on date of breathsampling^(§), N (%) Duration of mold-active antifungal 2 (2, 11; 2 (1,13; 0.52 exposure prior to breath sampling, 1, 205) 1, 345) days, median(IQR; range) *<500 neutrophils/mm³ for >10 days.²⁹ ^(†)Treatment withrecognized T-cell immunosuppressants, such as cyclosporine, TNF-αblockers, specific immunomodulating antibodies, or nucleoside analoguesduring the prior go days.²⁹ ^(‡)Exposure to corticosteroids at a meanminimum dose of 0.3 mg/kg/day of prednisone equivalent for >3 weeks.²⁹^(§)Specific antifungal agents included: voriconazole (N = 17),micafungin (N = 15), liposomal amphotericin B (N = 11), terbinafine (N =1), isavuconazole (N = 1), voriconazole and micafungin (N = 2),voriconazole and terbinafine (N = 2), posaconazole and liposomalamphotericin B (N = 1), and fluconazole (N = 1) in a patient withsuspected cryptococcal pneumonia.

TABLE 2 Invasive Fungal Disease Classification Invasive Aspergillosis (N= 34) 5 proven invasive aspergillosis 29 probable invasiveaspergillosis* 18 serum galactomannan index ≧ 0.5 4 Aspergillus speciesin respiratory tract cultures 4 serum galactomannan index ≧ 0.5 andAspergillus spp. in respiratory tract cultures 3 bronchoalveolar lavagefluid galactomannan index ≧ 0.5 Other Pneumonia (N = 30) 8 proveninvasive fungal disease 4 Mucorales 1 Cryptococcus neoformans 1 Fusariumproliferatum 1 Pseudallescheria boydii 1 unidentified invasivedematiaceous mold on lung biopsy 2 probable invasive fungal disease 1Paecilomyces variotii 1 Histoplasma capsulatum 20 possible invasivefungal disease^(†) *One patient had concurrent probable invasiveaspergillosis and Pneumocystis jirovecii pneumonia. ^(†) Streptococcuspneumoniae pneumonia (N = 1), Stenotrophomonas maltophilia pneumonia (N= 1), methicillin-resistant Staphylococcus aureus septic pulmonaryemboli (N = 1), coagulase-negative staphylococcus septic pulmonaryemboli (N = 1), and Enterococcus faecalis septic pulmonary emboli (N =1). The specific underlying cause of pneumonia in the remaining 15patients was not identified.

While monoterpene metabolites produced in vitro by A. fumigatus(camphene, α-pinene, β-pinene, and limonene) were equally present in thebreath of patients with or without IA, the volatile sesquiterpenesecondary metabolites β-trans-bergamotene and α-trans-bergamotene andtwo related metabolites that we did not observe in vitro, the terpenoidketone trans-geranylacetone and a β-vatirenene-like sesquiterpene,distinguished the breath of patients with IA from patients without IA(FIG. 13). No sesquiterpene compounds were present in ambient aircontrol samples. This A. fumigatus secondary metabolite signaturedistinguished patients with IA from patients with other IFD or othertypes of pneumonia with 94% (95% CI 81%-98%) sensitivity and 93% (95% CI79%-98%) specificity utilizing the reference standard of proven orprobable IA by EORTC/MSG consensus criteria (Table 3). The smallestlesion we detected through breath metabolite analysis was 0.88 cm³ in alung transplant patient with probable IA.

TABLE 3 Breath Aspergillus fumigatus Metabolite Signature by theReference Standard and Test Parameters Invasive Other AspergillosisPneumonia A. fumigatus metabolite signature+ 32 2 34 A. fumigatusmetabolite signature− 2 28 30 34 30 64 Test Parameters Sensitivity (95%CI) 0.94 (0.81, 0.98) Specificity (95% CI) 0.93 (0.79, 0.98) PositiveLikelihood Ratio (95% CI) 14.1 (3.69, 54.0) Negative Likelihood Ratio(95% CI) 0.063 (0.02, 0.24) 

A. niger, which emits a distinct VOC profile from A. fumigatus in vitro(FIGS. 18A-D), was ultimately identified as the causal etiology ofpneumonia in one of the two patients with ‘probable’ IA whose breathsample lacked the A. fumigatus volatile secondary metabolite signature.Interestingly, we detected a novel sesquiterpene compound in thispatient's breath that we did not detect in the headspace gas of in vitrocultures of this patient's fungal isolate. On the other hand, there arelimitations of the EORTC/MSG reference standard for the diagnosis of IA,which relies on the sensitivity of fungal antigens and cultures for theclassification of ‘probable’ IA.²⁹ One patient with breathβ-trans-bergamotene and trans-geranylacetone was classified as having‘possible’ IFD during his lifetime, with pulmonary nodules butunrevealing respiratory tract cultures and negative fungal antigentesting. On autopsy, however, these pulmonary nodules contained invasiveseptate hyphal forms with acute-angle branching, which were identifiedas Aspergillus by immunohistochemical staining by the CDC InfectiousDiseases Pathology Branch.

We found no association between the contents of the last meal prior tobreath sampling, tobacco use, concurrently administered inhaled, oral,or topical medications and detection of this Aspergillus volatilesecondary metabolite signature.

Antifungal Exposure Experiments.

Patients were evaluated over time to determine the response toantifungal therapy; the A. fumigatus metabolite signature describedherein was evaluated over time as follows.

We assessed whether we could modulate the A. fumigatus VOC metabolomewith voriconazole, micafungin, and liposomal amphotericin B antifungaldrug exposure. We inoculated 10⁴ A. fumigatus Af293 and A1163 conidiainto YPD broth and incubated these cultures at 37° C. at 250 rpm for 48hours, then exposed these 48 hour hyphae to an inhibitory dose (1.0μg/mL) of voriconazole (Pfizer Inc., New York, N.Y.), micafungin,liposomal amphotericin (both Astellas Pharma US, Inc., Northbrook,Ill.), or no antifungal therapy for 12 hours, in 4 technical replicates,with matched media controls exposed to the same conditions. VOCs in theheadspace of each vial were extracted onto thermal desorption tubes.Cultures and media samples were incubated at 37° C. at 250 rpm foranother 36 hours, with repeat extraction of the headspace gas ontothermal desorption tubes.

As shown in FIGS. 14 and 20, in the patients who were sampled over time,the abundance of the VOC signature declined with effective antifungaltherapy, disappearing a few weeks into treatment.

Discussion

We identified distinctive terpene secondary metabolites in the volatilemetabolome of the most common pathogenic Aspergilli in vitro, and foundthat the A. fumigatus-specific VOCs β-trans-bergamotene,α-trans-bergamotene, a β-vatirenene-like sesquiterpene, andtrans-geranylacetone comprise a fungal metabolic signature that can beused to discriminate patients with IA from patients with other types ofpneumonia accurately, in a heterogeneous population at risk for IA. Ourresults suggest that direct detection of exogenous fungal metabolites inbreath, a matrix continuous with the primary site of infection, can beused as a novel, noninvasive, species-specific approach to identifyingpatients with IA, potentially allowing more precise targeting ofantifungal therapy and fewer invasive diagnostic procedures.

While microbial VOC detection in the breath has been suggested for thediagnosis of tuberculosis, Pseudomonas aeruginosa pneumonia, and IA,³²these studies have proposed compounds that are either common primarymetabolites or catabolic products of many microbial species or compoundsthat lack biologically plausible synthetic pathways as biomarkers ofdisease and are most likely contaminants or artifacts of samplecollection.³³ As an example, 2-pentylfuran, a breakdown product of thecommon fatty acid linoleic acid, was previously proposed as a breathbiomarker for IA,^(34, 35) but has since been shown to be widely presentin food products and ambient air,³⁵ and not detected in other series³⁶or in patient breath samples from our study. Other studies have takenhypothesis-free, pattern-based feature classification approaches todiscriminating infected and noninfected patients without identificationof the specific biologic components distinguishing these groups,increasing the risk of incorrectly identifying signal in noise andlimited reproducibility.^(32, 37)

In contrast to these studies, we took a biologically-guided approach tobiomarker identification. We identified volatile secondary terpenemetabolites released during growth of A. fumigatus and were able tomodulate secondary metabolite production with various stress conditionsand antifungal drug exposure in vitro, suggesting a biologicrelationship between the living, metabolically active organism andproduction of these compounds. Knowledge of these unique terpenemetabolites then informed our identification of these fungal secondarymetabolites in patient breath samples, and allowed the identification ofrelated compounds such as a β-vatirenene-like sesquiterpene andtrans-geranylacetone, potentially reflecting activation of these fungalsecondary metabolite pathways, silent under our in vitro cultureconditions, in the human lung milieu.

Other groups have previously identified sesquiterpenes in the in vitrovolatome of A. fumigatus, ^(36, 38, 39) and one group performed a seriesidentifying a sesquiterpene compound in the breath of 8 IA patients,³⁶although the dominant metabolite, β-trans-bergamotene, was misidentifiedas β-farnesene in these studies, given the similarity in fragmentationpatterns of these compounds and the absence of β-trans-bergamotene fromthe NIST library. In our study, and in a concurrent independentassessment of the in vitro A. fumigatus volatome (Drs. ChristophHeddergott and Jean Paul Latgé, personal communication), the NISTlibrary provisionally identified β-trans-bergamotene as β-farnesene.When we spiked a pure β-farnesene standard into a culture of A.fumigatus to confirm the identity of this metabolite, the retention timeof β-farnesene and our endogenous sesquiterpene were clearly distinct.In contrast, we observed augmentation of this endogenous sesquiterpenewith the addition of a β-trans-bergamotene standard, and perfectretention time and spectral pattern alignment with this endogenoussesquiterpene. Interestingly, A. fumigatus production ofβ-trans-bergamotene has been known since at least 1976,⁴⁰ although theenzyme that catalyzes the formation of this compound, a crypticβ-trans-bergamotene synthase, was only recently discovered in asecondary metabolite biosynthetic gene cluster.⁴¹ β-trans-bergamotene isputatively a precursor metabolite for fumagillin, a secondarymeroterpenoid metabolite with antibiotic and anti-angiogenicproperties.^(20, 41)

The biologic significance of these sesquiterpene products, whether asend-products themselves or as precursors to other secondary metabolites,and their role in fungal pathogenesis are yet undefined. While notrequired for primary growth of the organism, a substantial diversion ofresources away from primary metabolism is required for synthesis ofthese secondary metabolites, and many fungal species have evolved uniqueterpene cyclases with distinctive suites of sesquiterpene products ofgreat structural and stereochemical diversity.^(18, 19, 23, 42) Theseproducts are believed to have roles in inter- and intraspeciescommunication, deterring competing microorganisms in the environment andpotentially contributing to survival of the organism in the mammalianhost.^(18, 21-23)

Based on the marked interspecies diversity of sesquiterpene productionin vitro, we believe the secondary metabolite signature identified in IApatients in this study is likely specific for A. fumigatus, the dominantcause of IA¹⁴. Other Aspergillus species likely have their owndistinctive volatile secondary metabolite signatures in vivo. With theadvent of galactomannan testing, proven IA cases and cases withspecies-level Aspergillus identification are increasingly rare, but thebreath metabolite signature identified all of the galactomannan-positiveprobable IA cases suggesting A. fumigatus as the causative species. A.flavus, terreus, or calidoustus were not identified as the causalspecies of any IA cases at our institution over the study period.

These findings provide proof-of-concept that direct detection ofexogenous fungal metabolites in breath can be used as a noninvasiveapproach to identifying the underlying microbial etiology of pneumonia.GC-MS or real-time gas sensors, e.g., point-of-care, bedside diagnostictests, can be used to detect IA based on the detection of specificmicrobial volatile signatures.

In addition, the abundance of the VOC signature declined with effectiveantifungal therapy, disappearing a few weeks into treatment, as shown inFIGS. 14 and 20.

Results:

The monoterpenes camphene, α- and β-pinene, and limonene, andsesquiterpene compounds α- and β-trans-bergamotene were distinctivevolatile metabolites of A. fumigatus in vitro, distinguishing A.fumigatus from other pathogenic Aspergilli. Of 64 patients, 34 werediagnosed with invasive aspergillosis, while 30 were ultimatelydiagnosed with other causes of pneumonia, including other invasivemycoses. A signature of the sesquiterpene metabolitesα-trans-bergamotene and β-trans-bergamotene, a β-vatirenene-likesesquiterpene, and the sesquiterpene intermediate trans-geranylacetoneidentified patients with invasive aspergillosis with 94% sensitivity(95% confidence interval [CI], 81%-98%) and 93% specificity (95% CI,79%-98%).

Conclusions and Relevance

In patients with suspected fungal pneumonia, an A. fumigatus-specificsecondary metabolite signature in breath can identify individuals withinvasive aspergillosis. These results provide proof-of-concept thatdirect detection of exogenous fungal metabolites in breath can be usedas a novel, noninvasive, species-specific approach to identifying theprecise microbial cause of pneumonia.

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OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

1. A method for diagnosing a subject with invasive aspergillosis (IA),the method comprising: obtaining a sample comprising breath of a subjector suspected of comprising Aspergillus isolated from a subject;detecting the presence in the sample of one, two, three, or morevolatile organic compounds (VOCs) produced by the Aspergillus species ina sample comprising breath from the subject or headspace from a culturesuspected of comprising Aspergillus isolated from the subject, whereinthe VOCs are selected from the group consisting of camphene, α-pinene,β-pinene, limonene, α-trans-bergamotene, β-trans-bergamotene, andtrans-geranylacetone; and diagnosing a subject as having IA when thereare one, two, three or more of the VOCs present in the sample.
 2. Themethod of claim 1, comprising: (i) detecting the presence in the sampleof α-trans-bergamotene, β-trans-bergamotene, and trans-geranylacetone;and diagnosing a subject who has all three of α-trans-bergamotene,β-trans-bergamotene, and trans-geranylacetone in the sample as havingIA, e.g., wherein the sample is a sample of a subject's breath; or (ii)detecting the presence in the sample of camphene, α-pinene, β-pinene,limonene, α-trans-bergamotene, β-trans-bergamotene, andtrans-geranylacetone; and diagnosing a subject who has all of camphene,α-pinene, β-pinene, limonene, α-trans-bergamotene, β-trans-bergamotene,and trans-geranylacetone, e.g., wherein the sample comprises headspacefrom a culture.
 3. The method of claim 1, comprising: obtaining a samplecomprising breath of a subject or headspace from a culture suspected ofcomprising Aspergillus isolated from a subject; detecting the presencein the sample of one, two, three, or more VOCs selected from the groupconsisting of camphene, α-pinene, β-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, and trans-geranylacetone; andadministering an antifungal treatment to a subject who hasα-trans-bergamotene, β-trans-bergamotene, and trans-geranylacetone intheir breath or camphene, α-pinene, β-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, and trans-geranylacetone inheadspace from a culture.
 4. The method of claim 3, wherein thetreatment comprises administration of one or more doses of one or moreantifungal compounds.
 5. A method of detecting the presence of anAspergillus fumigatus, A. terreus, or A. calidoustus infection in asubject, the method comprising: obtaining a sample comprising breath ofa subject, or headspace from a culture suspected of comprisingAspergillus isolated from a subject; determining the presence of one,two, three, or more of the VOCs selected from the group consisting ofcamphene, α-pinene, β-pinene, limonene, α-trans-bergamotene,β-trans-bergamotene, trans-geranylacetone, elixene, alpha-santalene,beta-elemene, acoradien, chamigrene, 1,5,9-trimethyl cyclododecatriene,9-decene-2-one and beta-sesquiphellandrene in the sample, wherein: thepresence of one, two, three, or more of camphene, α-pinene, β-pinene,limonene, α-trans-bergamotene, β-trans-bergamotene, andtrans-geranylacetone indicates the presence of an A. fumigatusinfection; the presence of one, two, three, or more of elixene,alpha-santalene, beta-elemene, acoradien, chamigrene, and1,5,9-trimethyl cyclododecatriene indicates the presence of an A.terreus infection; and the presence of one or both of 9-decene-2-one andbeta-sesquiphellandrene indicates the presence of an A. calidoustusinfection in the subject.
 6. The method of claim 5, further comprisingselecting, and optionally administering, a therapy comprising an azolefor a subject who has an A. fumigatus or A. terreus infection; orselecting, and optionally administering, a therapy comprisingamphotericin B (AMB) for a subject who has an A. calidoustus infection.7. A method of monitoring efficacy of a treatment for invasiveaspergillosis (IA) in a subject, the method comprising: determining afirst level of one, two, three, or more volatile organic compounds(VOCs) produced by the Aspergillus species in a sample comprising breathfrom the subject or headspace from a culture suspected of comprisingAspergillus isolated from the subject, wherein the VOCs are selectedfrom the group consisting of camphene, α-pinene, β-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, trans-geranylacetone, elixene,alpha-santalene, beta-elemene, acoradien, chamigrene, 1,5,9-trimethylcyclododecatriene, 9-decene-2-one and beta-sesquiphellandrene, in thesubject; administering a treatment for IA to the subject; determining asecond level of the VOCs in a sample obtained after administration ofthe treatment to the subject; and comparing the first and second levelsof VOCs, wherein a decrease in the VOCs indicates that the treatment hasbeen effective in treating the IA in the subject, and an increase or nochange indicates that the treatment has not been effective in treatingthe IA in the subject.
 8. The method of claim 6, wherein the treatmentcomprises administration of one or more doses of one or more antifungalcompounds.
 9. (canceled)
 10. A method of detecting the presence of anAspergillus fumigatus, A. terreus, or A. calidoustus infection in aculture, the method comprising: obtaining a sample comprising gas fromthe headspace of the culture; determining the presence of one, two,three, or more, e.g., all, of the VOCs selected from the groupconsisting of camphene, α-pinene, β-pinene, limonene,α-trans-bergamotene, β-trans-bergamotene, trans-geranylacetone, elixene,alpha-santalene, beta-elemene, acoradien, chamigrene, 1,5,9-trimethylcyclododecatriene, 9-decene-2-one and beta-sesquiphellandrene in thesample, wherein: the presence of one, two, three, or more of α-pinene,β-pinene, limonene, α-trans-bergamotene, β-trans-bergamotene,trans-geranylacetone indicates the presence of A. fumigatus in theculture; the presence of one, two, three, or more of elixene,alpha-santalene, beta-elemene, acoradien, chamigrene, and1,5,9-trimethyl cyclododecatriene indicates the presence of A. terreusin the culture; and the presence of one or both of 9-decene-2-one andbeta-sesquiphellandrene indicates the presence of A. calidoustusinfection in the culture.
 11. The method of claim 1, wherein determiningthe presence of a VOC comprises assaying the sample to detect thepresence the VOC.
 12. The method of claim 11, wherein assaying thesample to detect the presence the VOC comprises using a gaschromatography (GC) or spectrometry method.
 13. The method of claim 12,wherein the spectrophotometry method is mobility spectrometry (IMS) ordifferential mobility spectrometry (DMS).
 14. The method of claim 1,wherein the subject is a human.
 15. The method of claim 11, wherein thesubject is a human.
 16. The method of claim 4, wherein the antifungalcompound is an amphotericin B formulation; an azole antifungal compound;or an echinocandin antifungal compound.